19-50849771-A-T

Position:

• chr19-50849771-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000598079.1(ENSG00000267968):​n.214-1140A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.894 in 151,164 control chromosomes in the GnomAD database, including 60,594 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.89 (60594 hom., cov: 25)
• Consequence: ENSG00000267968 ENST00000598079.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.804

Genes affected

ENSG00000267968 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.916 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372441	NR_131203.1	n.214-1140A>T		intron_variant
LOC105372441	NR_131205.1	n.231-1140A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000267968	ENST00000598079.1	n.214-1140A>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.894 AC: 135058 AN: 151048 Hom.: 60559 Cov.: 25

Gnomad AFR AF: 0.863

Gnomad AMI AF: 0.915

Gnomad AMR AF: 0.823

Gnomad ASJ AF: 0.923

Gnomad EAS AF: 0.842

Gnomad SAS AF: 0.863

Gnomad FIN AF: 0.962

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.923

Gnomad OTH AF: 0.896

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.894 AC: 135146 AN: 151164 Hom.: 60594 Cov.: 25 AF XY: 0.891 AC XY: 65840 AN XY: 73866

Gnomad4 AFR AF: 0.863

Gnomad4 AMR AF: 0.823

Gnomad4 ASJ AF: 0.923

Gnomad4 EAS AF: 0.842

Gnomad4 SAS AF: 0.863

Gnomad4 FIN AF: 0.962

Gnomad4 NFE AF: 0.923

Gnomad4 OTH AF: 0.898

Alfa AF: 0.911 Hom.: 7942

Bravo AF: 0.880

Asia WGS AF: 0.866 AC: 3011 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.40
DANN	Benign	0.39

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs266867; hg19: chr19-51353027;